Are you sure you have the skip shader at all? When I first tried it, I ran into an odd problem — a large horizontal hint (à la Casa) caused the map to be pitch black. Turned out that even though I could select skip in the Radiant texture menu, the actual shader was missing, resulting in skip-covered faces being rendered as the “shader not found” texture, which killed off the skybox… Had to google the shader and add it manually to common.shader (the file I found had antiportal too, also missing in my cobbled-together installation):